Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: anhydro-N-acetylmuramoyl-L-alanine amidase



Gene: amiD Accession Numbers: G6452 (EcoCyc), b0867, ECK0858

Synonyms: ybjR

Regulation Summary Diagram: ?

Summary:
AmiD is an 1,6-anhydro-N-acetylmuramic acid (anhMurNAc)-L-alanine amidase responsible for cleaving the bond between muramic acid and L-alanine within murein, muropeptides, and anhydro-muropeptides.

AmiD is an outer membrane lipoprotein [Juncker03, Uehara07]. Structures of AmiD have been determined to resolutions of 1.8 and 2.2 Å and are available in the RCSB Protein Data Bank, though the results have not been published yet.

nagB nagZ ampD amiD mutants are unable to release murein tripeptide from GlcNAc-anhMurNAc-tripeptide while the nagB nagZ ampD mutant is able to do so [Uehara07]. Assays of purified AmiD show it prefers GlcNAc-anhMurNAc-peptides or GlcNAc-MurNAc-peptides as substrates over those lacking GlcNAc [Uehara07].

Purified AmiD was shown to hydrolyse peptidoglycan fragments that have at least three amino acids in their peptide chains and the enzyme activity was inhibited by its substrate invitro [Pennartz09].

Review: [Park08]

Locations: outer membrane

Map Position: [904,136 -> 904,966] (19.49 centisomes)
Length: 831 bp / 276 aa

Molecular Weight of Polypeptide: 31.072 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002947 , EchoBASE:EB3451 , EcoGene:EG13687 , EcoliWiki:b0867 , ModBase:P75820 , OU-Microarray:b0867 , PortEco:amiD , PR:PRO_000022093 , Pride:P75820 , Protein Model Portal:P75820 , RefSeq:NP_415388 , RegulonDB:G6452 , SMR:P75820 , String:511145.b0867 , Swiss-Model:P75820 , UniProt:P75820

Relationship Links: InterPro:IN-FAMILY:IPR002477 , InterPro:IN-FAMILY:IPR002502 , PDB:Structure:2BH7 , PDB:Structure:2WKX , PDB:Structure:3D2Y , PDB:Structure:3D2Z , Pfam:IN-FAMILY:PF01510 , Prosite:IN-FAMILY:PS51257 , Smart:IN-FAMILY:SM00644

In Paralogous Gene Group: 218 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009253 - peptidoglycan catabolic process Inferred from experiment Inferred by computational analysis [GOA01a, Uehara07]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Uehara07]
GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Uehara07]
GO:0009392 - N-acetyl-anhydromuramoyl-L-alanine amidase activity Inferred from experiment [Uehara07]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0019867 - outer membrane Inferred from experiment [Uehara07]
GO:0009279 - cell outer membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, Uehara07]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: cell structure membrane
cell structure murein
metabolism degradation of macromolecules proteins/peptides/glycopeptides

Essentiality data for amiD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Credits:
Curated 11-Apr-2006 by Keseler I , SRI International
Last-Curated ? 05-Nov-2007 by Johnson A , JCVI


Enzymatic reaction of: anhydro-N-acetylmuramoyl-L-alanine amidase

GlcNAc-1,6-anhMurNAc-L-Ala-γ-D-Glu-DAP-D-Ala + H2O <=> N-acetyl-β-D-glucosamine(anhydrous)-N-acetylmuramate + L-Ala-γ-D-Glu-meso-DAP-D-Ala

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: anhydromuropeptides recycling

Cofactors or Prosthetic Groups: Zn2+ [Uehara07]

T(opt): 43 °C [BRENDA14, vanHeijenoort75]

pH(opt): 8.3 [BRENDA14, vanHeijenoort75]


Sequence Features

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 16 prolipoprotein signal sequence
[Uehara07]
 
Lipid-Binding-Site 17  
[UniProt10]
UniProt: N-palmitoyl cysteine; Non-Experimental Qualifier: by similarity;
Chain 17 -> 276  
[UniProt09]
UniProt: N-acetylmuramoyl-L-alanine amidase amiD;
Metal-Binding-Site 50  
[UniProt11]
UniProt: Zinc; catalytic.
Protein-Segment 51 -> 52  
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Active-Site 119  
[Kerff10, UniProt11]
UniProt: Proton acceptor.
Metal-Binding-Site 166  
[UniProt10a]
UniProt: Zinc;
Amino-Acid-Site 174  
[UniProt11]
UniProt: Transition state stabilizer; Sequence Annotation Type: site.
Metal-Binding-Site 176  
[UniProt10a]
UniProt: Zinc;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Juncker03: Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A (2003). "Prediction of lipoprotein signal peptides in Gram-negative bacteria." Protein Sci 12(8);1652-62. PMID: 12876315

Kerff10: Kerff F, Petrella S, Mercier F, Sauvage E, Herman R, Pennartz A, Zervosen A, Luxen A, Frere JM, Joris B, Charlier P (2010). "Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family." J Mol Biol 397(1);249-59. PMID: 20036252

Park08: Park JT, Uehara T (2008). "How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan)." Microbiol Mol Biol Rev 72(2);211-27, table of contents. PMID: 18535144

Pennartz09: Pennartz A, Genereux C, Parquet C, Mengin-Lecreulx D, Joris B (2009). "Substrate-induced inactivation of the Escherichia coli AmiD N-acetylmuramoyl-L-alanine amidase highlights a new strategy to inhibit this class of enzyme." Antimicrob Agents Chemother 53(7);2991-7. PMID: 19237650

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Uehara07: Uehara T, Park JT (2007). "An anhydro-N-acetylmuramyl-L-alanine amidase with broad specificity tethered to the outer membrane of Escherichia coli." J Bacteriol 189(15);5634-41. PMID: 17526703

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

vanHeijenoort75: van Heijenoort J, Parquet C, Flouret B, van Heijenoort Y (1975). "Envelope-bound N-acetylmuramyl-L-alanine amidase of Escherichia coli K 12. Purification and properties of the enzyme." Eur J Biochem 1975;58(2);611-9. PMID: 1102308

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, BIOCYC13B.